LAMMPS (7 Aug 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93)
  using 1 OpenMP thread(s) per MPI task
# 250 toluene system for drude polarizability example (Nose-Hoover)

units real
boundary p p p

atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls
improper_style fourier
special_bonds lj/coul 0.0 0.0 0.5

pair_style lj/cut/thole/long 2.600 8.0 8.0
pair_modify mix geometric tail yes
kspace_style pppm 1.0e-4

read_data data.toluene extra/special/per/atom 1
  orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287)
  2 by 1 by 2 MPI processor grid
  reading atoms ...
  5500 atoms
  scanning bonds ...
  4 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  8 = max dihedrals/atom
  scanning impropers ...
  2 = max impropers/atom
  reading bonds ...
  5500 bonds
  reading angles ...
  6000 angles
  reading dihedrals ...
  6000 dihedrals
  reading impropers ...
  1500 impropers
  5 = max # of 1-2 neighbors
  10 = max # of 1-3 neighbors
  16 = max # of 1-4 neighbors
  20 = max # of special neighbors
  special bonds CPU = 0.000718355 secs
  read_data CPU = 0.0167146 secs

comm_modify vel yes

group gTOLUENE molecule 1:250
5500 atoms in group gTOLUENE
group gCORES type 1 2 3 4 5 6 7
3750 atoms in group gCORES
group gDRUDES type 8 9 10 11 12
1750 atoms in group gDRUDES

pair_coeff    1    1 0.069998 3.550000 1.620000 # CAT CAT
pair_coeff    1    2 0.069998 3.550000 1.620000 # CAT CAO
pair_coeff    1    3 0.069998 3.550000 1.620000 # CAT CAM
pair_coeff    1    4 0.069998 3.550000 1.620000 # CAT CAP
pair_coeff    1    5 0.067968 3.524911 1.620000 # CAT CTT
pair_coeff    1    6 0.045825 2.931041 0.000000 # CAT HAT
pair_coeff    1    7 0.045825 2.931041 0.000000 # CAT HT
pair_coeff    2    2 0.069998 3.550000 1.620000 # CAO CAO
pair_coeff    2    3 0.069998 3.550000 1.620000 # CAO CAM
pair_coeff    2    4 0.069998 3.550000 1.620000 # CAO CAP
pair_coeff    2    5 0.067968 3.524911 1.620000 # CAO CTT
pair_coeff    2    6 0.045825 2.931041 0.000000 # CAO HAT
pair_coeff    2    7 0.045825 2.931041 0.000000 # CAO HT
pair_coeff    3    3 0.069998 3.550000 1.620000 # CAM CAM
pair_coeff    3    4 0.069998 3.550000 1.620000 # CAM CAP
pair_coeff    3    5 0.067968 3.524911 1.620000 # CAM CTT
pair_coeff    3    6 0.045825 2.931041 0.000000 # CAM HAT
pair_coeff    3    7 0.045825 2.931041 0.000000 # CAM HT
pair_coeff    4    4 0.069998 3.550000 1.620000 # CAP CAP
pair_coeff    4    5 0.067968 3.524911 1.620000 # CAP CTT
pair_coeff    4    6 0.045825 2.931041 0.000000 # CAP HAT
pair_coeff    4    7 0.045825 2.931041 0.000000 # CAP HT
pair_coeff    5    5 0.065997 3.500000 1.620000 # CTT CTT
pair_coeff    5    6 0.044496 2.910326 0.000000 # CTT HAT
pair_coeff    5    7 0.044496 2.910326 0.000000 # CTT HT
pair_coeff    6    6 0.029999 2.420000 0.000000 # HAT HAT
pair_coeff    6    7 0.029999 2.420000 0.000000 # HAT HT
pair_coeff    7    7 0.029999 2.420000 0.000000 # HT HT
pair_coeff    1    8 0.000000 0.000000 1.620000 # CAT D_CAT
pair_coeff    1    9 0.000000 0.000000 1.620000 # CAT D_CAO
pair_coeff    1   10 0.000000 0.000000 1.620000 # CAT D_CAM
pair_coeff    1   11 0.000000 0.000000 1.620000 # CAT D_CAP
pair_coeff    1   12 0.000000 0.000000 1.620000 # CAT D_CTT
pair_coeff    2    8 0.000000 0.000000 1.620000 # CAO D_CAT
pair_coeff    2    9 0.000000 0.000000 1.620000 # CAO D_CAO
pair_coeff    2   10 0.000000 0.000000 1.620000 # CAO D_CAM
pair_coeff    2   11 0.000000 0.000000 1.620000 # CAO D_CAP
pair_coeff    2   12 0.000000 0.000000 1.620000 # CAO D_CTT
pair_coeff    3    8 0.000000 0.000000 1.620000 # CAM D_CAT
pair_coeff    3    9 0.000000 0.000000 1.620000 # CAM D_CAO
pair_coeff    3   10 0.000000 0.000000 1.620000 # CAM D_CAM
pair_coeff    3   11 0.000000 0.000000 1.620000 # CAM D_CAP
pair_coeff    3   12 0.000000 0.000000 1.620000 # CAM D_CTT
pair_coeff    4    8 0.000000 0.000000 1.620000 # CAP D_CAT
pair_coeff    4    9 0.000000 0.000000 1.620000 # CAP D_CAO
pair_coeff    4   10 0.000000 0.000000 1.620000 # CAP D_CAM
pair_coeff    4   11 0.000000 0.000000 1.620000 # CAP D_CAP
pair_coeff    4   12 0.000000 0.000000 1.620000 # CAP D_CTT
pair_coeff    5    8 0.000000 0.000000 1.620000 # CTT D_CAT
pair_coeff    5    9 0.000000 0.000000 1.620000 # CTT D_CAO
pair_coeff    5   10 0.000000 0.000000 1.620000 # CTT D_CAM
pair_coeff    5   11 0.000000 0.000000 1.620000 # CTT D_CAP
pair_coeff    5   12 0.000000 0.000000 1.620000 # CTT D_CTT
pair_coeff    8    8 0.000000 0.000000 1.620000 # D_CAT D_CAT
pair_coeff    8    9 0.000000 0.000000 1.620000 # D_CAT D_CAO
pair_coeff    8   10 0.000000 0.000000 1.620000 # D_CAT D_CAM
pair_coeff    8   11 0.000000 0.000000 1.620000 # D_CAT D_CAP
pair_coeff    8   12 0.000000 0.000000 1.620000 # D_CAT D_CTT
pair_coeff    9    9 0.000000 0.000000 1.620000 # D_CAO D_CAO
pair_coeff    9   10 0.000000 0.000000 1.620000 # D_CAO D_CAM
pair_coeff    9   11 0.000000 0.000000 1.620000 # D_CAO D_CAP
pair_coeff    9   12 0.000000 0.000000 1.620000 # D_CAO D_CTT
pair_coeff   10   10 0.000000 0.000000 1.620000 # D_CAM D_CAM
pair_coeff   10   11 0.000000 0.000000 1.620000 # D_CAM D_CAP
pair_coeff   10   12 0.000000 0.000000 1.620000 # D_CAM D_CTT
pair_coeff   11   11 0.000000 0.000000 1.620000 # D_CAP D_CAP
pair_coeff   11   12 0.000000 0.000000 1.620000 # D_CAP D_CTT
pair_coeff   12   12 0.000000 0.000000 1.620000 # D_CTT D_CTT


neighbor 2.0 bin

variable vTEMP   equal 260.0
variable vTEMP_D equal 1.0
variable vPRESS  equal 1.0

velocity gCORES  create ${vTEMP} 12345
velocity gCORES  create 260 12345
velocity gDRUDES create ${vTEMP_D} 12345
velocity gDRUDES create 1 12345

fix fDRUDE all drude C C C C C N N D D D D D

fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8
  1250 = # of size 2 clusters
  0 = # of size 3 clusters
  250 = # of size 4 clusters
  0 = # of frozen angles
  find clusters CPU = 0.000344038 secs

compute cTEMP_CORE gCORES temp/com
compute cTEMP all temp/drude

fix fDIRECT all drude/transform/direct
fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0
fix fNVT1 gCORES nvt temp 260 ${vTEMP} 100.0
fix fNVT1 gCORES nvt temp 260 260 100.0
fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0
fix fNVT2 gDRUDES nvt temp 1 ${vTEMP_D} 20.0
fix fNVT2 gDRUDES nvt temp 1 1 20.0
fix fINVERSE all drude/transform/inverse

fix fMOMENTUM all momentum 100 linear 1 1 1

thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2]
thermo 50

timestep 0.5
run 2000
PPPM initialization ...
  using 12-bit tables for long-range coulomb (src/kspace.cpp:323)
  G vector (1/distance) = 0.382011
  grid = 40 40 40
  stencil order = 5
  estimated absolute RMS force accuracy = 0.0325934
  estimated relative force accuracy = 9.8154e-05
  using double precision FFTW3
  3d grid and FFT values/proc = 34263 16000
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 19
New max number of 1-2 to 1-4 neighbors: 20 (+1)
Neighbor list info ...
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 10
  ghost atom cutoff = 10
  binsize = 5, bins = 8 8 8
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut/thole/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 18 | 18 | 18 Mbytes
Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] 
       0    11086.347    2910.7282    202.07402    8175.6191    6565.4851    20.333365 1.0706727e-06     -3299.85    4972.8631    1306116.6   -1306199.8     40273.68    48631.318    314.89553    3.1777821 
      50     3563.376    4630.6343    321.47655   -1067.2583    735.72048    604.78665    689.14826    -3277.411    815.58183    1306088.7   -1306723.8    17813.425    48631.318      503.827 0.0087118179 
     100    3327.4722    4395.1107    305.12559   -1067.6385    597.93175    651.62645     945.4151   -3267.2851    584.58833    1306135.9   -1306715.8    17407.335    48631.318     478.2017 0.0075985638 
     150    3036.9065    4740.2304    329.08513   -1703.3238    558.64983    619.91284    658.80686   -3278.7837    285.12462      1306173     -1306720    18448.248    48631.318    515.75286 0.0063215227 
     200    2697.9581    4559.3445    316.52734   -1861.3864    522.09335     593.8913    754.61446     -3273.49    87.660464    1306183.9     -1306730    17888.937    48631.318    496.07143  0.006870622 
     250    2348.7563     4410.585    306.19988   -2061.8288    506.05006    575.35172    715.55055   -3276.3261   -18.364482    1306177.3   -1306741.4    11592.049    48631.318    479.88562 0.0071741023 
     300    2019.8256    4040.1415    280.48225   -2020.3159    604.30771    641.66688    693.93802   -3278.5312   -115.73639    1306183.2   -1306749.1    3631.3625    48631.318    439.57995 0.0069886424 
     350    1699.5169    3944.9851    273.87613   -2245.4682    452.07416    638.06529    658.79116   -3279.6053   -157.07584    1306196.9   -1306754.6    13544.368    48631.318    429.22695 0.0062868216 
     400    1399.2927     3726.098    258.68014   -2326.8053    457.91943    621.44727    639.39905   -3279.2395   -188.85912    1306185.4   -1306762.8    10792.273    48631.318    405.41133 0.0059340084 
     450    1120.5246     3518.345    244.25712   -2397.8204    519.48859     584.6579    646.36688   -3278.6685   -289.59912    1306184.1   -1306764.2    2755.5597    48631.318    382.80717  0.005570751 
     500    868.01643    3359.8794    233.25583    -2491.863    460.73928    581.49568    581.01732   -3281.5544   -252.20168    1306184.3   -1306765.7     6120.364    48631.318    365.56528 0.0058756204 
     550    637.01646    3214.9521    223.19441   -2577.9356    431.81484    578.87415    540.94046   -3281.5337   -266.36074    1306182.8   -1306764.5    8622.4353    48631.318    349.79661 0.0058589476 
     600    418.04028    3113.4063    216.14471   -2695.3661    430.45936    538.68158    522.24597    -3283.456   -311.87897    1306174.3   -1306765.8    7068.9275    48631.318    338.74796 0.0059567639 
     650    218.59562    2930.8439    203.47052   -2712.2482    514.47296     514.2838    551.52551   -3282.0904   -405.37401    1306164.5   -1306769.5   -13.554086    48631.318    318.88481 0.0052667849 
     700    45.227739    2830.1443    196.47957   -2784.9165    451.11157    498.26426    541.18833   -3282.1427   -375.95321    1306157.1   -1306774.4    3947.6268    48631.318    307.92741 0.0068018884 
     750   -114.28676    2798.3154    194.26988   -2912.6022    412.75298    503.28782    481.32167   -3284.3411   -393.53987      1306147   -1306779.1    7143.3424    48631.318    304.46466 0.0061596613 
     800   -263.63827    2694.8085    187.08403   -2958.4468    455.67916    487.49754    476.86576   -3284.3133   -451.95784      1306145   -1306787.2    1185.9474    48631.318    293.20289 0.0058203323 
     850   -397.71592    2559.1922    177.66903   -2956.9082    458.83313    481.22619    478.31233    -3284.068   -437.26509    1306138.6   -1306792.6    346.80221    48631.318    278.44747 0.0054921238 
     900   -515.18134    2544.8753    176.67509   -3060.0567     395.0016     457.5898    446.68361    -3285.485   -423.56234    1306145.1   -1306795.3    3712.8594    48631.318    276.88864 0.0074054726 
     950   -617.28607    2451.1721    170.16985   -3068.4582     383.6428    446.59872    434.46241   -3285.1348   -391.59326    1306142.3   -1306798.7    5429.2191    48631.318    266.69429 0.0057487961 
    1000   -703.15541    2334.8366    162.09339    -3037.992    424.34957    462.21115    451.80811   -3284.3803   -426.53346    1306133.9   -1306799.3    1137.6144    48631.318    254.03671 0.0053915025 
    1050   -771.17572    2303.8364    159.94123   -3075.0121    426.21406    436.50744    435.10013   -3285.1938   -411.13999    1306125.6   -1306802.1    1636.9467    48631.318    250.66288 0.0069341736 
    1100   -822.72317     2283.421    158.52392   -3106.1442    376.67703    447.77728    418.45763   -3286.5919   -377.48075    1306118.9   -1306803.8    4760.4718    48631.318    248.44134 0.0074024122 
    1150   -857.06061    2259.0725    156.83355   -3116.1331    400.31517    431.65949    457.68078   -3285.1977   -430.47775    1306115.8   -1306805.9    3194.5159    48631.318    245.79231  0.007063706 
    1200   -875.50971    2238.2632    155.38889   -3113.7729    445.38534    460.97161    432.10511   -3285.4238   -472.46582    1306114.7     -1306809   -653.49627    48631.318    243.52813 0.0071446561 
    1250   -880.37609     2294.689    159.30619   -3175.0651    411.35498    444.73774    420.06429   -3286.0366   -458.05353    1306104.4   -1306811.5    945.79687    48631.318    249.66483  0.011854196 
    1300   -871.31122    2284.2295    158.58005   -3155.5407    404.97869    441.75305    426.34479   -3285.4859   -424.79602    1306094.8   -1306813.2    4406.6128    48631.318     248.4856  0.084411062 
    1350   -816.69657    2325.9211    161.47444   -3142.6176    696.85542    442.50059    431.19981   -3285.7859   -450.27129    1305836.1   -1306813.3    593.86622    48631.318    251.40736    2.9289249 
    1400   -794.25213    2263.5122    157.14177   -3057.7643     645.6531     466.2204    446.22253   -3285.1821   -420.65316    1305903.7   -1306813.8    1386.3481    48631.318    245.20568    1.8917548 
    1450    -776.1076    2287.6591    158.81814   -3063.7667     427.0331    479.10417    439.67675   -3285.9536   -395.13308    1306087.6   -1306816.1    2936.7117    48631.318    248.87185  0.061341392 
    1500   -725.48032    2371.4108    164.63251   -3096.8911    390.03135    464.30817    446.91941   -3284.7808   -393.16302    1306095.4   -1306815.6    3544.3635    48631.318    258.01262  0.011585228 
    1550   -671.48696    2315.9233    160.78035   -2987.4102    457.04771    500.26018     464.7623    -3284.931   -400.98142    1306091.7   -1306815.3    2052.6204    48631.318    251.97656 0.0094518433 
    1600   -618.82679    2449.0893    170.02525   -3067.9161    425.47171    474.66369    471.99137   -3284.3677    -430.3224    1306091.3   -1306816.6    441.31257    48631.318    266.46283  0.014263201 
    1650   -567.82233    2425.2281    168.36872   -2993.0504    421.02008    511.26686    463.22202   -3285.0378   -377.24205    1306088.4   -1306814.7    5198.6214    48631.318    263.83232  0.074728934 
    1700   -502.46013    2441.8437    169.52224   -2944.3039    642.39863    512.90005    490.39655    -3283.975   -417.39351    1305929.1   -1306817.7    1141.2401    48631.318    264.52268    2.0436397 
    1750   -459.52135    2499.0847    173.49613    -2958.606    679.34078    505.30943    484.78276   -3284.6269   -384.28217    1305861.7   -1306820.8    1527.0852    48631.318    270.10144    3.1876179 
    1800   -471.14322    2476.2445    171.91047   -2947.3877    442.48278     530.4566     474.0343   -3284.0957   -371.97492    1306084.3   -1306822.6    3392.0306    48631.318    269.36641    0.1041603 
    1850   -462.80151    2536.7173    176.10873   -2999.5188    437.07855    525.05914    474.07725   -3283.7908   -422.22641    1306091.6   -1306821.3    1630.1204    48631.318    275.99568  0.016808725 
    1900    -469.8785    2468.9596    171.40473   -2938.8381     446.7879     531.6128    496.02681   -3284.2335   -395.17163    1306085.7   -1306819.6    3119.2384    48631.318    268.62462  0.014603394 
    1950   -491.07182    2445.6794    169.78853   -2936.7512    457.80204    527.21208     470.1608   -3283.9622   -391.90163    1306101.9     -1306818    1122.0978    48631.318    266.08919  0.018903661 
    2000   -518.41243     2418.604    167.90885   -2937.0165    415.92605    536.62844    480.48912   -3283.7876   -363.72641    1306096.2   -1306818.7    4474.8778    48631.318    263.07743   0.13492637 
Loop time of 22.3198 on 4 procs for 2000 steps with 5500 atoms

Performance: 3.871 ns/day, 6.200 hours/ns, 89.606 timesteps/s
98.3% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 11.452     | 12.249     | 12.556     |  13.2 | 54.88
Bond    | 0.71352    | 0.72923    | 0.74557    |   1.3 |  3.27
Kspace  | 5.7189     | 6.0293     | 6.8195     |  18.6 | 27.01
Neigh   | 0.44028    | 0.44044    | 0.44065    |   0.0 |  1.97
Comm    | 0.39667    | 0.40817    | 0.41558    |   1.1 |  1.83
Output  | 0.0019479  | 0.0032187  | 0.0068657  |   3.7 |  0.01
Modify  | 2.413      | 2.4256     | 2.4347     |   0.5 | 10.87
Other   |            | 0.0349     |            |       |  0.16

Nlocal:    1375 ave 1407 max 1349 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Nghost:    8082.5 ave 8114 max 8047 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs:    325715 ave 343636 max 314954 min
Histogram: 1 1 0 1 0 0 0 0 0 1

Total # of neighbors = 1302860
Ave neighs/atom = 236.884
Ave special neighs/atom = 15.6364
Neighbor list builds = 44
Dangerous builds = 0
Total wall time: 0:00:22
